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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 21-33557226-AC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=33557226&ref=AC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 33557226,
"ref": "AC",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000356577.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.6233delC",
"hgvs_p": "p.Pro2078fs",
"transcript": "NM_138927.4",
"protein_id": "NP_620305.3",
"transcript_support_level": null,
"aa_start": 2078,
"aa_end": null,
"aa_length": 2426,
"cds_start": 6233,
"cds_end": null,
"cds_length": 7281,
"cdna_start": 6288,
"cdna_end": null,
"cdna_length": 8393,
"mane_select": "ENST00000356577.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.6233delC",
"hgvs_p": "p.Pro2078fs",
"transcript": "ENST00000356577.10",
"protein_id": "ENSP00000348984.4",
"transcript_support_level": 1,
"aa_start": 2078,
"aa_end": null,
"aa_length": 2426,
"cds_start": 6233,
"cds_end": null,
"cds_length": 7281,
"cdna_start": 6288,
"cdna_end": null,
"cdna_length": 8393,
"mane_select": "NM_138927.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.6233delC",
"hgvs_p": "p.Pro2078fs",
"transcript": "ENST00000300278.8",
"protein_id": "ENSP00000300278.2",
"transcript_support_level": 1,
"aa_start": 2078,
"aa_end": null,
"aa_length": 2303,
"cds_start": 6233,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 6262,
"cdna_end": null,
"cdna_length": 7477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.317delC",
"hgvs_p": "p.Pro106fs",
"transcript": "ENST00000381692.6",
"protein_id": "ENSP00000371111.2",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 454,
"cds_start": 317,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 358,
"cdna_end": null,
"cdna_length": 2463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.416delC",
"hgvs_p": "p.Pro139fs",
"transcript": "ENST00000421541.1",
"protein_id": "ENSP00000405807.1",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 343,
"cds_start": 416,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 416,
"cdna_end": null,
"cdna_length": 1151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "n.6233delC",
"hgvs_p": null,
"transcript": "ENST00000455528.5",
"protein_id": "ENSP00000399783.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.6233delC",
"hgvs_p": "p.Pro2078fs",
"transcript": "NM_032195.3",
"protein_id": "NP_115571.3",
"transcript_support_level": null,
"aa_start": 2078,
"aa_end": null,
"aa_length": 2303,
"cds_start": 6233,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 6288,
"cdna_end": null,
"cdna_length": 7503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.6233delC",
"hgvs_p": "p.Pro2078fs",
"transcript": "NM_001291411.2",
"protein_id": "NP_001278340.2",
"transcript_support_level": null,
"aa_start": 2078,
"aa_end": null,
"aa_length": 2108,
"cds_start": 6233,
"cds_end": null,
"cds_length": 6327,
"cdna_start": 6288,
"cdna_end": null,
"cdna_length": 7897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.6233delC",
"hgvs_p": "p.Pro2078fs",
"transcript": "ENST00000381679.8",
"protein_id": "ENSP00000371095.4",
"transcript_support_level": 5,
"aa_start": 2078,
"aa_end": null,
"aa_length": 2108,
"cds_start": 6233,
"cds_end": null,
"cds_length": 6327,
"cdna_start": 6261,
"cdna_end": null,
"cdna_length": 7860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.3215delC",
"hgvs_p": "p.Pro1072fs",
"transcript": "ENST00000436227.5",
"protein_id": "ENSP00000400985.1",
"transcript_support_level": 5,
"aa_start": 1072,
"aa_end": null,
"aa_length": 1453,
"cds_start": 3215,
"cds_end": null,
"cds_length": 4362,
"cdna_start": 3217,
"cdna_end": null,
"cdna_length": 5269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.317delC",
"hgvs_p": "p.Pro106fs",
"transcript": "ENST00000704334.1",
"protein_id": "ENSP00000515848.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 487,
"cds_start": 317,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 2354,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "c.317delC",
"hgvs_p": "p.Pro106fs",
"transcript": "NM_001291412.3",
"protein_id": "NP_001278341.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 454,
"cds_start": 317,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 372,
"cdna_end": null,
"cdna_length": 2477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "n.317delC",
"hgvs_p": null,
"transcript": "ENST00000695559.1",
"protein_id": "ENSP00000512016.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"hgvs_c": "n.6288delC",
"hgvs_p": null,
"transcript": "NR_103797.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SON",
"gene_hgnc_id": 11183,
"dbsnp": "rs886039779",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.801,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000356577.10",
"gene_symbol": "SON",
"hgnc_id": 11183,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.6233delC",
"hgvs_p": "p.Pro2078fs"
}
],
"clinvar_disease": "Failure to thrive,Global developmental delay,ZTTK syndrome",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "ZTTK syndrome|Failure to thrive;Global developmental delay",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}